The Alchemist: Genesis
by Phantom Pendragon
Summary: When the Doctor recives a strange message from an unknown foe, he didn't know what he was getting into. T to be safe. Please Read and Review
1. Trouble

**Hello, thank you for bothering to check out this story. This is the first story in a, hopefully, long line of them. For those who like random backgrounds on fanfiction, continue reading. For the rest of you, skip ahead to the rest of the story. **

**The idea for **_**The Alchemist**_** has been bouncing around for quite some time. I have had tons of ideas of how to use his character, but then I realized that he had to be explained. So, this story came about. Each chapter is going to be rather short, 1, 500 words or so. I'm not sure how many chapters there will be yet, but hopefully a substantial amount. Anyway, please enjoy **_**The Alchemist: Genesis**_** and please Rate and Review.**

**-The Wandering Alchemist**

Chapter One: Trouble

The sound echoed among the high ceiling hallway, something between an old engine running and a gasping, wheezing breath. That sound meant many different things to many different people. To some it was fear, death and hate. To others it was joy, excitement and adventure. However, no matter where it was or who heard it, one meaning never changed: Trouble. As the T.A.R.D.I.S materialized, the sound slowly faded into silence. The door swung inward and the Doctor stepped out. His eyes glanced around excitedly, taking in all that was around him. He straightened his brown coat, tightened his bow tie, checked his for his sonic screwdriver and closed the T.A.R.D.I.S door behind him.

The hallway he stood in had a high, circular ceiling. The architecture was all curved, even the support beams, which arched from the sides of the hallway to create a passageway. At the top of these supports, two more curved out in an opposite direction and attached to the ceiling. Everything was white, and had a plastic look to it.

The Doctor stepped over to the wall and gave it to hard rap with his knuckle. "That's strange," he murmured to himself. "It's not alianium or crosivum, this is something… new."

Reaching into his pocket, he drew out his psychic paper. A well detailed map appeared before his eyes, replacing the coordinates that had been there before. This was not something of the Doctors imagining, this was a message. From who and why; well, he was about to find out. He figured it was a trap, set by one of his enemies. The Doctor, however, could never resist a trap.

The Doctor set off down the massive hall, following the map easily, as the hallway he was supposed to take was filled in with yellow. The hall was littered with large semi-circle doors, all of which he could not resist trying to open.

As he approached the first one, he gave it a quick examination. No handle, no button, no panel and no obvious way to open it at all. "Motion activated?" the Doctor asked, "or voice?" After waving his hands in front of the door he suddenly shouted, "Pineapple!" followed by, "Raxacoricofallapatorius! He waved it over the door and then stared at it intently for a few seconds.

"Genetic lock…" he murmured. He gave a second wave of his screwdriver. "And a deadlock… a deadlock deactivated by a genetic code, and reactivated once you owner of the genetic code passes by. Genetic deadlocks…. Will surprises never cease?"

The Doctor resumed his stride, waving his screwdriver at every door he passed. "Deadlocked, deadlocked, deadlocked," he chanted as he received the readings. "And what do you know! This one is deadlocked too! I guess someone doesn't want me snooping around too much. "

He walked on. The hallway never seemed to end. What was worse was that it had no windows, just door after door after door. The Doctor knew he was on a space station, the coordinates made that clear. He also knew that the station was nearly the size of a planet.

_A needle in a haystack, _the Doctor mused to himself_, except the needle is an unknown force drawing me to the haystack which happens to be a space station the size of a planet and the needle gave me a map to tell me exactly where to go. Yeah; there went the analogy._

At last, the Doctor reached the end of the hall. A door, slightly larger than the others he had passed, stood before him. The Doctor glanced at his map; it had vanished.

"Alright then," he said, nearly in a whisper. "Let's see what's behind door number one…"

He stepped forward, and the door silently split into four sections, two going into the wall and two going towards the ceiling. The Doctor strode confidently into the room. It was large, circular and mostly empty. All it contained were two curved chairs that rose up from the floor. One of these chairs had an occupant.

The occupant gave a series of clacking and humming noises that sounded as if they were some type of speech. The Doctor's casual attitude suddenly vanished, instantly replaced by a tension that was evident in his voice.

"That's impossible," he said. "I know every language; I should know what you're saying. Why don't I know what you're saying? "

"The universe is large, Time Lord," the thing said, switching to English. "Don't flatter yourself by thinking you know everything."

The Doctor sized the creature up. It was humanoid, but the Doctor figured it would stand about seven feet tall if it had not been sitting. It wore long, flowing silver robes and appeared to be male. His hands were long, thin and had fingernails like claws. His defining feature, however, was his face. He had three eyes, two in the "usual" place and one in the center of his forehead. The bottom two were blue while the top eye was green. The head was bald, or shaven, the Doctor wasn't sure. The Creature gestured too the chair across from him.

"Please, sit," he said. "It's not everyday I get to entertain a Time Lord, especially one of your reputation."

Cautiously, the Doctor sat down. "So," the Doctor began, "let me guess, psychic race? I scanned your station, no readings of a transmitter powerful enough to get a message on the psychic paper from this distance."

"You are correct, Doctor," said the creature. "But if we had such a transmitter, you would not have found it on your scanner. We are skilled at keeping secrets."

"I'll bet," said the Doctor. He was about ask his next question, when the alien cut him off.

"I am Jar'Keel," said the creature.

"Right, psychic," mumbled the doctor, "I'll have to get used to that." Speaking quickly, attempting to get his words out before Jar'Keel could cut him off again, he asked another question. "You misread my mind, Jar'Keel, or at least left a bit out. I was going to ask who and what you are."

"We are, we have been, we will be," said Jar'Keel. "Ah ha," said the doctor. "There's a "we" and I gather you're immortal. Well, big deal. It doesn't matter how you say it, but you're talking to a Time Lord, it's not that impressive."

Jar'Keel gave a light, harsh laugh. "You have quite the reputation, but your arrogance is… greater than expected. But I suspect this arrogance is because of fear, Time Lord. The Doctor, the last of the Time Lords', the Oncoming Storm! The legendary hero of a thousand tales is afraid."

The Doctor gritted his teeth. "Yeah," he said, quietly. "Yeah, I'm afraid. But as I told someone once, 'scared keeps you fast'."

"That din't help the poor soul you gave that advice to much, did it?" said Jar' Keel with a condescending tone.

The Doctor gritted his teeth and decided to change the subject.

"So," he said, "you must have some reason for drawing me here, besides gloating, that is."

"Quite right, Time Lord," said Jar'Keel. "We need you to assist in an… experiment."

The Doctor raised his eyebrows. He did not like the pause that came before the word "experiment."

"A strange mysterious force summons me to a planet sized space station just for an experiment? I never get this lucky," he said, rather cynically.

Jar'Keel rose from his seat. "Come, Doctor," he said. "I will show you the results of our experiment thus far. Trust me, once you see what we are doing, you will gladly support us."

Two sides of the Doctor fought within him that day. One was his old, battle hardened self that would never trust Jar'Keel, or nearly anyone else for that matter. The other was a younger Doctor; a Doctor who wanted to believe there was some good in the universe. The young Doctor won out, but not without some advice from his older counterpart.

The Doctor rose as well. "Alright, Jar'Keel, show me this "experiment," he said.

They headed out of the room and down another hallway. It was the same selection of doors, arched ceilings and plain white color.

"Well," said the Doctor, "you're certainly not picky about your architecture. The support beams look unique but everything else looks just… plain. I mean, if you're immortal, at least make sure the place you're going to be for eternity looks interesting. "

"We needed practicality," said the other. "The experiment is all that matters now. We have no need for things to look 'interesting.'"

They continued down the hall in silence after that, until they reached yet another non-descript door.

"This is it," said Jar'Keel.

"How do you blokes find your way about this place?" asked the Doctor. "I haven't seen a sign the whole trip."

"We have our ways, Doctor," said Jar'Keel.

"Ah, yes," said the Doctor. "Mysterious ways that must never be told, correct?"

"Something of the sort," said Jar'Keel.

He waved his long hand in front of the door and it slid open.

As they both stepped through the doorway, there was something the Doctor didn't know. This would be one of the defining moments of the universe and of his life. This would become a fixed point in time, a time when everything changed. The Doctor didn't know it, but he was about to change the fabric of the universe as he knew it. Why? Just because he took a single step.


	2. Fifty Seven

Chapter Two: Fifty Seven

At first glance the hallway looked like all the rest, long, high ceilinged and circular. But as they walked, the Doctor noticed glass windows, from floor to ceiling, inserted in regular places in the wall. As they approached one, the Doctor peered in.

It was a room mostly empty, except for one creature. It was a lizard like specimen, about the size of a small dog. The Doctor recognized it as a Flala, native to a planet many light years from his current position. And it was extinct in his current time frame. It sat in a corner, drinking out of a bowl of water, looking rather abandoned.

"What?" the doctor began to ask, but Jar'Keel cut him off.

"Patience, Doctor," said the creature. "All in good time."

They continued on throughout the room. There we're many more creatures in the glass rooms, some from thousands of years science their extinction, others thousands of years before they we're discovered. All looked scared, alone and abandoned.

"If you're trying to get me on your side, you're going about it the wrong way," said the Doctor. "Showing me a bunch of innocent creatures locked up in cages alone? What are you trying to do?"

"You shall see, Doctor," said Jar'Keel. "You shall see."

At last they reached the end of the hall. Unlike the others, the last glass room was dark. The Doctor got a sudden feeling of dread. A feeling that he should run, turn his back and flee. He fought it down however and stayed where he was.

"This, Doctor, is our experiment. This is our future… and yours," said Jar'Keel. And with those enigmatic words, he waved his hand over the glass.

The lights came on and the glass door split into four sections, much like the doors in the rest of the station. The room was plain and white, just like the others, but it featured a small hallway leading beyond the room.

Jar'Keel, waved his hand, ushering the Doctor forward.

The Doctor complied and led the way into the chamber. They followed the hallway a short distance until they came three a three pronged fork in the path.

"Take the left passage," said Jar'Keel. "He should be studying now."

_He? _Thought the doctor. _Studying? _

He took the left hallway and followed along until he reached his destination.

It was a massive room. All the walls we're lined with shelves, and on the shelves we're books. Books upon books upon books. There was a single desk against the wall. In it was a small figure that appeared to be reading a book and taking notes.

"Who is that?" the Doctor asked.

"I think he can introduce himself," said Jar'Keel. He clapped his hands once and the figure attempted to spin around in his chair.

"Fifty Seven," said Jar'Keel. "Come meet our guest."

Fifty seven walked up to the pair and proceeded to bow. As he did this, the Doctor sized him up.

He was a young boy, appearing to be somewhere around the ages of thirteen or fourteen. He had brown hair and brown eyes and had no truly defining features. He wore a robe that was the same silver-grey as Jar'Keel's, and the Doctor noticed that it had a hood. What confused him was the brown hair, why hadn't it been shaved like the others?

"Greetings, honored guest," said the boy as he bowed.

Instead of returning the bow, the Doctor stuck out his hand.

The boy pondered this for a moment before doing the same and shaking the Doctor's hand. "'The shaking of hands,'" the boy said, as if quoting something. "'It is a common way to greet many in the universe and originated on countless planets, prominent ones being Ralafax, Syrium and Earth.'"

"Well," said the Doctor smiling, "you sure know your history on strange topics. I'm the Doctor, pleasure to meet you Fifty Seven.'

"It is indeed a pleasure," said Fifty Seven. He said it out of formality, but the Doctor saw something in the deep brown eyes that hinted at a deeper meaning.

"Fifty Seven," said Jar'Keel, "please proceeded to your training quarters and begin your instruction. We shall join you in a moment."

"Yes, Jar'Keel," said Fifty Seven and bowed, which Jar'Keel returned. He began to bow to the Doctor, who cut him off with another handshake. The boy smiled and left the library.

Once they we're alone, Jar'Keel Spoke. "I sense you have many questions," he said. "Please, ask them."

"Ok," said the Doctor. "Where is the experiment?"

"That was it," said Jar'Keel.

"You're telling me," said the Doctor, "that little boy is your grand experiment?"

"He may lack height," said Jar'Keel, "but he is far from a 'boy', He is ninety four years old, going by your colander."

"He ages well," said the Doctor. "But in what way is he an experiment? And why does he wear your robes, but is not one of you? And why do you need me?"

"Those," said Jar'Keel," are questions that are better to be discovered than answered."

Before the Doctor could demand an answer, the other waved his arm in a way that meant 'follow me'.

They walked back to the fork in the hallway and this time to the right hand passage. As they walked, the Doctor tried to keep his mind from jumping to conclusions. Thankfully, he didn't have to try very long, as something of great interest was happening in front of him.

The room they stepped into was not as large as the library and not nearly as inviting. It was round and featured racks along the walls instead of shelves. The racks we're filled with weapons of all kinds. Swords, crossbows, daggers, knives, guns and other implements of death lined the walls. In the center of the room stood Fifty Seven.

Stood, however, may not be the right word. Fifty Seven was a whirlwind of action. He held no weapons of his own, but his opponent did. His opponent, an agile, robotic looking thing, wielded a spear. It was obviously a real one, and the robot was attempting to skewer the boy on every thrust. It didn't appear likely that he would succeed, however.

Fifty Seven was dodging left and right, rolling under high sweeps of the spear and leaping over low swipes. The robot surged forward suddenly, stabbing forward and then slashing upwards in an attempt to gut the boy.

The boy side stepped, grabbed the spear and used it to throw himself forward. His shoulder slammed into his foe, making him stagger. In a series of lighting fast movements, Fifty Seven grabbed the spear shaft near the blade and snapped it free of the rest of the spear with a sweep of his hand. He then ducked and twirled under his foe's swinging arms, appearing behind him. With one, deft strike, Fifty Seven buried the blade into the back of his opponents head.

The robot tumbled forward and hit the ground with a heavy _thunk. _The boy grabbed the spear and yanked it free from his foe's head. He then proceeded to take both ends of the spear and toss them in a hole in the wall, which the Doctor assumed was a trash can.

Suddenly, the robot twitched. Fifty Seven strode over to it and grabbed one of it's arms. The robot responded and the boy helped him up.

"Excellent match, Jar'Fifty Seven," said the robot in a synthesized tone.

"Same to you," said the boy. "You nearly had me there a few times."

The pair proceeded to analyze their battle and compare notes with each other. During this process the Doctor looked on in disbelief.

"That thing just tried to kill him and he's congratulating it?" the doctor said, astounded. "Not only that, but he's giving it tip's on how to beat him next time?"

"Yes, Fifty Seven is the most promising warrior yet. We've used the FT 2.0 model for many years, but Fifty Seven is the only one who has managed to survive every time," said Jar'Keel. "He has also formed somewhat of a bond with him, we're unsure of why, but we think it may have been the update to FT's programming.

Jar'Keel looked over at the Doctor. "Are you not impressed?" asked Jar'Keel. "A great warrior like yourself, I would have thought you would enjoy his victory."

"Enjoy it?" the doctor asked. "You nearly killed him! You we're trying to kill him!" The Doctors voice was filled with anger.

"Ah," said Jar'Keel. "There it is. There is the Doctor the legends speak of. Two hearts full of rage and destruction!"

"You're reading the wrong history books," retorted the Doctor. "But I still don't know why! Why did you bring me here? Why are you training that boy? Why did you have all those species? Why is all of this going on?"

As he was shouting, the Doctor had begun to feel a buzzing in his ear. As he finished, it had moved to the front of his skull. As it intensified, he began to lose feeling in his fingers and toes, like anesthesia. Then it crept up his legs and arms, making him fall to his knees. He was about to ask what was happening when he realized he couldn't move his mouth. As he fell face forward on the ground he could hear Jar'Keel in his head. The voice carried a knowing smirk.

All in good time, Time Lord, and you will have plenty of it from now on.

The Doctor lost consciousness with a knowing chuckle in his ears.


End file.
